Adding functional ingredients is an important method to develop functional dairy products. Mulberry pomace (MPo), a byproduct of mulberry fruit processing, is rich in phenolic compounds and anthocyanins and can be served as the functional ingredient in functional dairy products. The aim of this work was to prepare a functional flavored yogurt by incorporating MPo into stirred yogurt and to investigate the effects of MPo on the physicochemical and textural properties of the product during cold storage. We supplemented MPo powder up to 3% (wt/wt) in fermented milk, and the changes in color, pH, titratable acidity (TA), total phenol content (TPC), total anthocyanin content (TAC), water-holding capacity, rheological behavior, texture, and microstructure of the functional flavored yogurt were monitored during storage under 4°C for 28 d. The MPo powder brought a pink to dark red color to the yogurt, decreased the lightness (L*) and yellow-blue color (b*) values, increased the red-green color (a*) values, decreased the pH value, and increased the contents of TA, TPC, and TAC in a dose-dependent manner. The addition of MPo at 1%, 2%, and 3% (wt/wt) significantly increased water-holding capacity, consistency, viscosity, and viscosity index, and reduced firmness of yogurt samples. Supplementation of MPo significantly reduced the pore spaces and channels inside the samples and improved microstructure of the functional yogurt. During the 28 d of cold storage, MPo-fortified yogurt samples kept relatively constant color, although their L*, a*, and b* showed a decreasing tendency. The pH of all yogurt samples gradually decreased with increasing of TA. Interestingly, TPC and TAC contents and the texture parameters of MPo-fortified yogurt increased gradually and continuously during the 28 d of cold storage. Mulberry pomace is beneficial to improve the physicochemical and textural properties of yogurt and has the potential as a natural stabilizer to be used in functional yogurt rich in phytochemicals.